Methods and devices for determining a guest structure on a host structure

1. A method for determining a presence of at least one guest structure at a host structure, the method comprising steps of:

receiving light from the host structure at a light sensitive system, wherein the host structure is hosting one or more optically active entities at at least one part of the host structure not hosting the at least one guest structure, wherein the optically active entities cause light emission from said at least one part of the host structure,

outputting an output signal by said light sensitive system based on the received light,

determining a light value based on the output signal, the light value indicating an amount of light from the host structure incident on the light-sensitive system, and

determining on the basis of the light value, at least one of a quantity and a position of the at least one guest structure at the host structure.

2. The method according to claim 1 , further comprising a step of:

determining a binding property of the at least one guest structure in respect of the host structure on the basis of the light value.

3. The method according to claim 1 , wherein the light-sensitive system is part of a microscope, the method comprising:

determining image data based on the output signal, the image data representing an image of at least part of the host structure and comprising a plurality of image pixel values associated with respective parts of the host structure, wherein each image pixel value indicates an amount of light from its associated part of the host structure incident on the light-sensitive system; and

determining at least one region of interest (ROI) comprising at least one image pixel value in the image on the basis of the image pixel values, wherein the at least one ROI in the image indicates the position of the at least one guest structure at the host structure.

4. The method according to claim 3 , wherein determining the at least one ROI in the image comprises determining that said at least one image pixel value of the ROI is indicative of an amount of light that is lower than a threshold amount of light.

5. The method according to claim 4 , further comprising a step of:

determining a threshold pixel value indicating the threshold amount of light on the basis of the image data, and wherein the step of determining that said at least one image pixel value is indicative of the amount of light lower than the threshold amount of light comprises comparing the at least one image pixel value with the threshold pixel value, and wherein determining the threshold pixel value comprises

determining an average and a variation of image pixel values that are associated with respective parts of the host structure not hosting a guest structure; and

determining the threshold pixel value based on the determined average and variation.

6. The method according to claim 3 , wherein determining the image data based on the output signal comprises

determining for a plurality of time periods respective subsets of image data based on the output signal, wherein each subset of image data represents an image of at least part of the host structure during respective time periods, each subset of image data comprising a plurality of image pixel values associated with respective parts of the host structure, wherein each image pixel value in a subset of image data indicates an amount of light from its associated part of the host structure that is incident on the light-sensitive system during its associated time period, and

determining the image data based on the subsets of image data.

7. The method according to the claim 6 , wherein

each subset of image pixel values comprises a plurality of image pixel values associated with a light-emitting event during the time period, and wherein

determining the image data based on the subsets of image data further comprises:

fitting a point spread function for each light-emitting event in the subsets of image data, to its plurality of image pixel values for determining a position of each light-emitting event;

determining on the basis of the fitted point spread function for each light-emitting event in the subsets of image data, an event localization curve indicating a position of the light-emitting event, and

determining the image data comprising summing the determined event localization curves.

8. The method according to claim 1 , wherein a fractional occupation of the host structure by the optically active entities is below 20%.

9. The method according to claim 1 , further comprising

receiving reference light by the light-sensitive system from the host structure hosting one or more optically active entities, wherein the optically active entities cause light emission from the host structure and wherein the host structure hosts a reference quantity of guest structures,

outputting, by the light-sensitive system, a reference signal based on the received reference light,

determining a reference light value based on the output signal, the reference light value indicating an amount of light from the host structure incident on the light-sensitive system, and

determining on the basis of the light value and of the reference light value at least one of the quantity and the position of the at least one guest structure at the host structure.

10. The method according to claim 1 , wherein

the host structure is at least partially positioned in a fluid comprising optically active entities, the optically active entities being configured to transiently bind to the host structure.

11. The method according to claim 1 , further comprising applying a tension to the host structure by controlling a force application system, for at least one of

controlling the signal that is output by the light-sensitive system, and

suppressing a motion of the host structure.

12. The method according to claim 1 , wherein

the at least one guest structure comprises a protein and/or protein complex, and/or

the host structure is a DNA molecule, and/or

the optically active entities are DNA intercalator molecules, and/or

the light sensitive-system comprises an imaging system.

13. An optical system for determining a presence of at least one guest structure at a host structure, the optical system comprising:

a light-sensitive system configured to receive light from the host structure hosting one or more optically active entities at at least one part of the host structure not hosting the at least one guest structure, wherein the optically active entities cause light emission from said at least one part, and to output a signal based on the received light, and

the optical system further comprising a data processing system configured to perform the steps of:

determining a light value based on the output signal, the light value indicating an amount of light from the host structure incident on the light-sensitive system, and

determining on the basis of the light value at least one of a quantity and a position of the at least one guest structure at the host structure.

14. The optical system according to claim 13 , further comprising at least one of

an excitation light source for generating excitation light for exciting the one or more optically active entities hosted by the host structure,

a sample holder for holding the host structure,

a sample holder comprising a flow cell,

a first optical system for directing the excitation light towards the host structure,

a first optical system comprising a condenser lens for focusing the excitation light on the host structure,

a second optical system for directing light from said at least one part of the host structure to the light-sensitive system,

a second optical system comprising an objective lens,

a trap system for trapping at least one body in a trap attached to the host structure and

a force detection system for determining a force exerted by the trap on the trapped body.

15. A method for enabling determination of at least one of a quantity and a position of at least one guest structure at a host structure, the method comprising

combining the host structure hosting the at least one guest structure with a fluid and a plurality of optically active entities for causing the host structure to host one or more optically active entities at at least one part of the host structure not hosting the at least one guest structure, wherein the optically active entities cause light emission from said at least one part.

16. The method according to claim 1 , wherein the guest structure is a protein and/or protein complex and the host structure is a DNA-molecule.

17. The optical system according to claim 13 , wherein the guest structure is a protein and/or protein complex and the host structure is a DNA-molecule.

18. The method according to claim 7 , wherein the point spread function is a point spread function associated with the light-sensitive system, and wherein the fitting comprises selecting an amplitude and/or width of the point spread function.

19. The method according to claim 12 , wherein the DNA intercalator molecules are selected from the group consisting of YO-PRO molecules, SYTOX molecules and combinations thereof, and

the light sensitive-system comprises an imaging system selected from a CCD camera and a CMOS camera.

20. The method of claim 14 , wherein the trap is an optical and/or acoustic trap, and the trap system comprises means for positioning the trap.